Onconova Implementation Guide
0.2.0 - ci-build

Onconova Implementation Guide - Local Development build (v0.2.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Resource Profile: Genomic Variant Profile

Official URL: http://onconova.github.io/fhir/StructureDefinition/onconova-genomic-variant Version: 0.2.0
Active as of 2025-12-04 Computable Name: OnconovaGenomicVariant

A profile representing a genomic variant identified for a cancer patient.

This profile extends the base mCODE GenomicVariant profile (which in turn profiles the Genomics Reporting Variant profile) to include specific constraints and extensions relevant to Onconova.

Conformance:

Observation resources representing a genomic variant in the scope of Onconova SHALL conform to this profile. Any resource intended to conform to this profile SHOULD populate meta.profile accordingly.

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicVariant Variant
Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension Content/Rules for all slices
.... extension:secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
.... extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
.... extension:genomic-variant-assessment-date SO 0..1 dateTime Genomic Variant Assessment Date
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... Slices for category S 1..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text 0..1 string Plain text representation of the concept
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
... code SΣ 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69548-6
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... subject SOΣ 1..1 Reference(Cancer Patient Profile) Who and/or what the observation is about
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... focus Σ 0..* Reference(Resource) Not used in this profile
... encounter Σ 0..1 Reference(Encounter) Not used in this profile
... Slices for effective[x] SΣ 1..1 dateTime Clinically-relevant date of the genomic variant (e.g. the specimen collection date)
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime SOΣ 0..1 dateTime Clinically relevant time/time-period for observation
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... issued Σ 0..1 instant Not used in this profile
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Not used in this profile
... Slices for value[x] SΣC 0..1 CodeableConcept Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... interpretation 0..* CodeableConcept Not used in this profile
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
... bodySite 0..1 CodeableConcept Not used in this profile
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
... method S 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S 0..1 Reference(Human Specimen Profile) Not used in this profile
... device 0..1 Reference(Device | DeviceMetric) Not used in this profile
... Slices for component SΣ 4..* BackboneElement Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
.... component:conclusion-string Σ 0..1 BackboneElement Not used in this profile
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: conclusion-string
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:gene-studied SΣ 0..* BackboneElement Gene Studied
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48018-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
.... component:cytogenetic-location SOΣ 0..* BackboneElement Cytogenetic (Chromosome) Location
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48001-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Example: 1q21.1
.... component:reference-sequence-assembly OΣ 0..* BackboneElement Human Reference Sequence Assembly
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 62374-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
.... component:coding-hgvs OΣ 0..1 BackboneElement Coding (cDNA) Change - cHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:genomic-hgvs SOΣ 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81290-9
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:cytogenomic-nomenclature SΣ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81291-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
.... component:genomic-ref-seq OΣ 0..1 BackboneElement Genomic Reference Sequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48013-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:transcript-ref-seq OΣ 0..1 BackboneElement Reference Transcript
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:exact-start-end OΣ 0..1 BackboneElement Exact Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81254-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:inner-start-end OΣ 0..1 BackboneElement Inner Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81302-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:outer-start-end OΣ 0..1 BackboneElement Outer Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81301-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:coordinate-system OΣ 0..1 BackboneElement Coordinate System
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 92822-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
.... component:ref-allele Σ 0..1 BackboneElement Not used in this profile
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:alt-allele Σ 0..1 BackboneElement Not used in this profile
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69551-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:coding-change-type SOΣ 0..1 BackboneElement Coding DNA Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48019-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: Coding DNA Change Types Value Set (required)
.... component:genomic-source-class SOΣ 0..1 BackboneElement Genomic Source Class
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48002-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
.... component:sample-allelic-frequency SOΣ 0..1 BackboneElement Sample Allelic Frequency
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81258-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 Quantity Relative frequency in the sample
...... comparator ?!Σ 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... system ΣC 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
.... component:allelic-read-depth OΣ 0..1 BackboneElement Allelic Read Depth
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82121-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:allelic-state SOΣ 0..1 BackboneElement Allelic State
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 53034-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance OΣ 0..1 BackboneElement Variant Inheritance
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept variant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-inheritance
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: Variant Inheritances (extensible)
.... component:variation-code SOΣ 0..* BackboneElement Variation Code
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81252-9
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
.... component:chromosome-identifier OΣ 0..* BackboneElement Chromosome Identifier
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48000-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
.... component:protein-hgvs SOΣ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48005-3
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:amino-acid-change-type SOΣ 0..1 BackboneElement Amino Acid Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48006-1
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: Amino Acid Change Type Value Set (required)
.... component:molecular-consequence SOΣ 0..1 BackboneElement Molecular Consequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept molecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: molecular-consequence
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.
.... component:copy-number SOΣ 0..1 BackboneElement Genomic Structural Variant Copy Number
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82155-3
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣC 0..1 Quantity Actual component result
Constraints: cnt-3
.... component:variant-confidence-status OΣ 0..1 BackboneElement Variant Confidence Status
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-confidence-status
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
.... component:clinical-relevance SOΣ 1..1 BackboneElement Clinical relevance of the genomic variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: LL4034-6
....... display 1..1 string Representation defined by the system
Fixed Value: ACMG_Clinical significance of genetic variation
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 CodeableConcept Actual component result
Binding: Clinical Relevance Value Set (required)
.... component:nucleotides-count SOΣ 1..1 BackboneElement Length of of the variant in nNucleotides
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 integer Actual component result
.... component:gene-region SOΣ 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result
.... component:gene-panel-sequencing SOΣ 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C165600
....... display 1..1 string Representation defined by the system
Fixed Value: Tumor Panel Sequencing
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Sequencing Gene Panel
.... component:hgvs-version SOΣ 1..1 BackboneElement HGVS Version
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81303-0
....... display 1..1 string Representation defined by the system
Fixed Value: HGVS version [ID]
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result
.... component:rna-hgvs SOΣ 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: rna-hgvs
....... display 1..1 string Representation defined by the system
Fixed Value: Transcript RNA change (rHGVS)
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📦4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📦4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📦4.0.1 FHIR Std.
Observation.method Base extensible LOINC Answer Codes for LL4048-6 unknown?
Observation.component.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 unknown?
Observation.component:coding-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:exact-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 unknown?
Observation.component:ref-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base required Coding DNA Change Types Value Set 📦0.2.0 This IG
Observation.component:genomic-source-class.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 unknown?
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 unknown?
Observation.component:variant-inheritance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible Variant Inheritances 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variation-code.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 unknown?
Observation.component:protein-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:amino-acid-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​value[x] Base required Amino Acid Change Type Value Set 📦0.2.0 This IG
Observation.component:molecular-consequence.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:molecular-consequence.​value[x] Base extensible Molecular Consequence 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:copy-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:clinical-relevance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:clinical-relevance.​value[x] Base required Clinical Relevance Value Set 📦0.2.0 This IG
Observation.component:nucleotides-count.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-region.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-panel-sequencing.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:hgvs-version.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:rna-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
cnt-3 error Observation.component:copy-number.value[x] There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from GenomicVariant

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicVariant Variant
Constraints: o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
... Slices for extension Content/Rules for all slices
.... extension:genomic-variant-assessment-date SO 0..1 dateTime Genomic Variant Assessment Date
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... status 1..1 code Not used in this profile
... subject O 1..1 Reference(Cancer Patient Profile) Who and/or what the observation is about
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... encounter 0..1 Reference(Encounter) Not used in this profile
... effective[x] 1..1 dateTime Clinically-relevant date of the genomic variant (e.g. the specimen collection date)
... Slices for effective[x] Content/Rules for all slices
.... effective[x]:effectiveDateTime O 0..1 dateTime Clinically relevant time/time-period for observation
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... issued 0..1 instant Not used in this profile
... performer 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Not used in this profile
... interpretation 0..* CodeableConcept Not used in this profile
... bodySite 0..1 CodeableConcept Not used in this profile
... specimen 0..1 Reference(Human Specimen Profile) Not used in this profile
... device 0..1 Reference(Device | DeviceMetric) Not used in this profile
... component 4..* BackboneElement Component results
... Slices for component Content/Rules for all slices
.... component:conclusion-string 0..1 BackboneElement Not used in this profile
.... component:cytogenetic-location O 0..* BackboneElement Cytogenetic (Chromosome) Location
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:reference-sequence-assembly O 0..* BackboneElement Human Reference Sequence Assembly
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:coding-hgvs O 0..1 BackboneElement Coding (cDNA) Change - cHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T
.... component:genomic-hgvs O 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
.... component:genomic-ref-seq O 0..1 BackboneElement Genomic Reference Sequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:transcript-ref-seq O 0..1 BackboneElement Reference Transcript
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:exact-start-end O 0..1 BackboneElement Exact Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:inner-start-end O 0..1 BackboneElement Inner Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:outer-start-end O 0..1 BackboneElement Outer Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:coordinate-system O 0..1 BackboneElement Coordinate System
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:ref-allele 0..1 BackboneElement Not used in this profile
.... component:alt-allele 0..1 BackboneElement Not used in this profile
.... component:coding-change-type O 0..1 BackboneElement Coding DNA Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... value[x] 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: Coding DNA Change Types Value Set (required)
.... component:genomic-source-class O 0..1 BackboneElement Genomic Source Class
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:sample-allelic-frequency O 0..1 BackboneElement Sample Allelic Frequency
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:allelic-read-depth O 0..1 BackboneElement Allelic Read Depth
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:allelic-state O 0..1 BackboneElement Allelic State
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:variant-inheritance O 0..1 BackboneElement Variant Inheritance
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:variation-code O 0..* BackboneElement Variation Code
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:chromosome-identifier O 0..* BackboneElement Chromosome Identifier
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:protein-hgvs O 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
.... component:amino-acid-change-type O 0..1 BackboneElement Amino Acid Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... value[x] 1..1 CodeableConcept Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: Amino Acid Change Type Value Set (required)
.... component:molecular-consequence O 0..1 BackboneElement Molecular Consequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:copy-number O 0..1 BackboneElement Genomic Structural Variant Copy Number
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:variant-confidence-status O 0..1 BackboneElement Variant Confidence Status
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:clinical-relevance SO 1..1 BackboneElement Clinical relevance of the genomic variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: LL4034-6
....... display 1..1 string Representation defined by the system
Fixed Value: ACMG_Clinical significance of genetic variation
..... value[x] S 0..1 CodeableConcept Actual component result
Binding: Clinical Relevance Value Set (required)
.... component:nucleotides-count SO 1..1 BackboneElement Length of of the variant in nNucleotides
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
..... value[x] S 0..1 integer Actual component result
.... component:gene-region SO 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
..... value[x] S 0..1 string Actual component result
.... component:gene-panel-sequencing SO 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C165600
....... display 1..1 string Representation defined by the system
Fixed Value: Tumor Panel Sequencing
..... value[x] S 0..1 string Sequencing Gene Panel
.... component:hgvs-version SO 1..1 BackboneElement HGVS Version
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81303-0
....... display 1..1 string Representation defined by the system
Fixed Value: HGVS version [ID]
..... value[x] S 0..1 string Actual component result
.... component:rna-hgvs SO 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: rna-hgvs
....... display 1..1 string Representation defined by the system
Fixed Value: Transcript RNA change (rHGVS)
..... value[x] S 0..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.component:coding-change-type.​value[x] Base required Coding DNA Change Types Value Set 📦0.2.0 This IG
Observation.component:amino-acid-change-type.​value[x] Base required Amino Acid Change Type Value Set 📦0.2.0 This IG
Observation.component:clinical-relevance.​value[x] Base required Clinical Relevance Value Set 📦0.2.0 This IG

Constraints

Id Grade Path(s) Description Expression
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicVariant Variant
Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.
Additional BindingsPurpose
AllLanguages Max Binding
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
.... extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
.... extension:genomic-variant-assessment-date SO 0..1 dateTime Genomic Variant Assessment Date
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business Identifier for observation
... basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) Part of referenced event
... status ?!SΣ 1..1 code Not used in this profile
Binding: ObservationStatus (required): Codes providing the status of an observation.
... Slices for category S 1..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text 0..1 string Plain text representation of the concept
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text Σ 0..1 string Plain text representation of the concept
... code SΣ 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69548-6
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... subject SOΣ 1..1 Reference(Cancer Patient Profile) Who and/or what the observation is about
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... focus Σ 0..* Reference(Resource) Not used in this profile
... encounter Σ 0..1 Reference(Encounter) Not used in this profile
... Slices for effective[x] SΣ 1..1 dateTime Clinically-relevant date of the genomic variant (e.g. the specimen collection date)
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime SOΣ 0..1 dateTime Clinically relevant time/time-period for observation
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... issued Σ 0..1 instant Not used in this profile
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Not used in this profile
... Slices for value[x] SΣC 0..1 CodeableConcept Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... interpretation 0..* CodeableConcept Not used in this profile
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
... note 0..* CodedAnnotation Comments about the Observation that also contain a coded type
... bodySite 0..1 CodeableConcept Not used in this profile
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
... method S 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S 0..1 Reference(Human Specimen Profile) Not used in this profile
... device 0..1 Reference(Device | DeviceMetric) Not used in this profile
... referenceRange C 0..* BackboneElement Not used in this profile
Constraints: obs-3
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... low C 0..1 SimpleQuantity Low Range, if relevant
.... high C 0..1 SimpleQuantity High Range, if relevant
.... type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
.... appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
.... age 0..1 Range Applicable age range, if relevant
.... text 0..1 string Text based reference range in an observation
... hasMember Σ 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Not used in this profile
... derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
... Slices for component SΣ 4..* BackboneElement Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
..... value[x] Σ 0..1 Actual component result
...... valueQuantity Quantity
...... valueCodeableConcept CodeableConcept
...... valueString string
...... valueBoolean boolean
...... valueInteger integer
...... valueRange Range
...... valueRatio Ratio
...... valueSampledData SampledData
...... valueTime time
...... valueDateTime dateTime
...... valuePeriod Period
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:conclusion-string Σ 0..1 BackboneElement Not used in this profile
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: conclusion-string
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Summary conclusion (interpretation/impression)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:gene-studied SΣ 0..* BackboneElement Gene Studied
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48018-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:cytogenetic-location SOΣ 0..* BackboneElement Cytogenetic (Chromosome) Location
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48001-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Example: 1q21.1
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:reference-sequence-assembly OΣ 0..* BackboneElement Human Reference Sequence Assembly
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 62374-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coding-hgvs OΣ 0..1 BackboneElement Coding (cDNA) Change - cHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-hgvs SOΣ 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81290-9
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:cytogenomic-nomenclature SΣ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81291-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-ref-seq OΣ 0..1 BackboneElement Genomic Reference Sequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48013-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:transcript-ref-seq OΣ 0..1 BackboneElement Reference Transcript
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:exact-start-end OΣ 0..1 BackboneElement Exact Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81254-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:inner-start-end OΣ 0..1 BackboneElement Inner Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81302-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Imprecise variant inner-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:outer-start-end OΣ 0..1 BackboneElement Outer Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81301-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Imprecise variant outer-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coordinate-system OΣ 0..1 BackboneElement Coordinate System
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 92822-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:ref-allele Σ 0..1 BackboneElement Not used in this profile
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:alt-allele Σ 0..1 BackboneElement Not used in this profile
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69551-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coding-change-type SOΣ 0..1 BackboneElement Coding DNA Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48019-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: Coding DNA Change Types Value Set (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-source-class SOΣ 0..1 BackboneElement Genomic Source Class
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48002-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:sample-allelic-frequency SOΣ 0..1 BackboneElement Sample Allelic Frequency
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81258-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 Quantity Relative frequency in the sample
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
...... value Σ 0..1 decimal Numerical value (with implicit precision)
...... comparator ?!Σ 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... unit Σ 0..1 string Unit representation
...... system ΣC 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
...... code Σ 0..1 code Coded form of the unit
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:allelic-read-depth OΣ 0..1 BackboneElement Allelic Read Depth
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82121-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Quantity Unfiltered count of supporting reads
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:allelic-state SOΣ 0..1 BackboneElement Allelic State
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 53034-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variant-inheritance OΣ 0..1 BackboneElement Variant Inheritance
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept variant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-inheritance
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: Variant Inheritances (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variation-code SOΣ 0..* BackboneElement Variation Code
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81252-9
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:chromosome-identifier OΣ 0..* BackboneElement Chromosome Identifier
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48000-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:protein-hgvs SOΣ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48005-3
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:amino-acid-change-type SOΣ 0..1 BackboneElement Amino Acid Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48006-1
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: Amino Acid Change Type Value Set (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:molecular-consequence SOΣ 0..1 BackboneElement Molecular Consequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept molecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: molecular-consequence
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:copy-number SOΣ 0..1 BackboneElement Genomic Structural Variant Copy Number
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82155-3
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣC 0..1 Quantity Actual component result
Constraints: cnt-3
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variant-confidence-status OΣ 0..1 BackboneElement Variant Confidence Status
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-confidence-status
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:clinical-relevance SOΣ 1..1 BackboneElement Clinical relevance of the genomic variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: LL4034-6
....... display 1..1 string Representation defined by the system
Fixed Value: ACMG_Clinical significance of genetic variation
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 CodeableConcept Actual component result
Binding: Clinical Relevance Value Set (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:nucleotides-count SOΣ 1..1 BackboneElement Length of of the variant in nNucleotides
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 integer Actual component result
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:gene-region SOΣ 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:gene-panel-sequencing SOΣ 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C165600
....... display 1..1 string Representation defined by the system
Fixed Value: Tumor Panel Sequencing
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Sequencing Gene Panel
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:hgvs-version SOΣ 1..1 BackboneElement HGVS Version
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81303-0
....... display 1..1 string Representation defined by the system
Fixed Value: HGVS version [ID]
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:rna-hgvs SOΣ 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: rna-hgvs
....... display 1..1 string Representation defined by the system
Fixed Value: Transcript RNA change (rHGVS)
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.language Base preferred Common Languages 📦4.0.1 FHIR Std.
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📦4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📦4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📦4.0.1 FHIR Std.
Observation.method Base extensible LOINC Answer Codes for LL4048-6 unknown?
Observation.referenceRange.​type Base preferred Observation Reference Range Meaning Codes 📦4.0.1 FHIR Std.
Observation.referenceRange.​appliesTo Base example Observation Reference Range Applies To Codes 📦4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:conclusion-string.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:gene-studied.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:gene-studied.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:coding-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:coding-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:transcript-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 unknown?
Observation.component:coordinate-system.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base required Coding DNA Change Types Value Set 📦0.2.0 This IG
Observation.component:coding-change-type.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 unknown?
Observation.component:genomic-source-class.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 unknown?
Observation.component:allelic-state.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible Variant Inheritances 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variant-inheritance.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:variation-code.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variation-code.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 unknown?
Observation.component:chromosome-identifier.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:protein-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:protein-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​value[x] Base required Amino Acid Change Type Value Set 📦0.2.0 This IG
Observation.component:amino-acid-change-type.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:molecular-consequence.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:molecular-consequence.​value[x] Base extensible Molecular Consequence 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:molecular-consequence.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:molecular-consequence.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:copy-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:copy-number.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:copy-number.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variant-confidence-status.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:clinical-relevance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:clinical-relevance.​value[x] Base required Clinical Relevance Value Set 📦0.2.0 This IG
Observation.component:clinical-relevance.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:clinical-relevance.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:nucleotides-count.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:nucleotides-count.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:nucleotides-count.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:gene-region.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-region.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:gene-region.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:gene-panel-sequencing.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-panel-sequencing.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:gene-panel-sequencing.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:hgvs-version.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:hgvs-version.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:hgvs-version.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:rna-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:rna-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:rna-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
cnt-3 error Observation.component:copy-number.value[x] There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-3 error Observation.referenceRange Must have at least a low or a high or text low.exists() or high.exists() or text.exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from GenomicVariant

Summary

Mandatory: 6 elements
Must-Support: 19 elements

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicVariant Variant
Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension Content/Rules for all slices
.... extension:secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
.... extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
.... extension:genomic-variant-assessment-date SO 0..1 dateTime Genomic Variant Assessment Date
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... Slices for category S 1..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text 0..1 string Plain text representation of the concept
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
... code SΣ 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69548-6
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... subject SOΣ 1..1 Reference(Cancer Patient Profile) Who and/or what the observation is about
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... focus Σ 0..* Reference(Resource) Not used in this profile
... encounter Σ 0..1 Reference(Encounter) Not used in this profile
... Slices for effective[x] SΣ 1..1 dateTime Clinically-relevant date of the genomic variant (e.g. the specimen collection date)
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime SOΣ 0..1 dateTime Clinically relevant time/time-period for observation
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... issued Σ 0..1 instant Not used in this profile
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Not used in this profile
... Slices for value[x] SΣC 0..1 CodeableConcept Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... interpretation 0..* CodeableConcept Not used in this profile
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
... bodySite 0..1 CodeableConcept Not used in this profile
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
... method S 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S 0..1 Reference(Human Specimen Profile) Not used in this profile
... device 0..1 Reference(Device | DeviceMetric) Not used in this profile
... Slices for component SΣ 4..* BackboneElement Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
.... component:conclusion-string Σ 0..1 BackboneElement Not used in this profile
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: conclusion-string
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:gene-studied SΣ 0..* BackboneElement Gene Studied
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48018-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
.... component:cytogenetic-location SOΣ 0..* BackboneElement Cytogenetic (Chromosome) Location
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48001-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Example: 1q21.1
.... component:reference-sequence-assembly OΣ 0..* BackboneElement Human Reference Sequence Assembly
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 62374-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
.... component:coding-hgvs OΣ 0..1 BackboneElement Coding (cDNA) Change - cHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:genomic-hgvs SOΣ 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81290-9
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:cytogenomic-nomenclature SΣ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81291-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
.... component:genomic-ref-seq OΣ 0..1 BackboneElement Genomic Reference Sequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48013-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:transcript-ref-seq OΣ 0..1 BackboneElement Reference Transcript
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:exact-start-end OΣ 0..1 BackboneElement Exact Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81254-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:inner-start-end OΣ 0..1 BackboneElement Inner Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81302-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:outer-start-end OΣ 0..1 BackboneElement Outer Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81301-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:coordinate-system OΣ 0..1 BackboneElement Coordinate System
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 92822-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
.... component:ref-allele Σ 0..1 BackboneElement Not used in this profile
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:alt-allele Σ 0..1 BackboneElement Not used in this profile
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69551-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:coding-change-type SOΣ 0..1 BackboneElement Coding DNA Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48019-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: Coding DNA Change Types Value Set (required)
.... component:genomic-source-class SOΣ 0..1 BackboneElement Genomic Source Class
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48002-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
.... component:sample-allelic-frequency SOΣ 0..1 BackboneElement Sample Allelic Frequency
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81258-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 Quantity Relative frequency in the sample
...... comparator ?!Σ 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... system ΣC 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
.... component:allelic-read-depth OΣ 0..1 BackboneElement Allelic Read Depth
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82121-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:allelic-state SOΣ 0..1 BackboneElement Allelic State
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 53034-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance OΣ 0..1 BackboneElement Variant Inheritance
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept variant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-inheritance
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: Variant Inheritances (extensible)
.... component:variation-code SOΣ 0..* BackboneElement Variation Code
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81252-9
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
.... component:chromosome-identifier OΣ 0..* BackboneElement Chromosome Identifier
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48000-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
.... component:protein-hgvs SOΣ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48005-3
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:amino-acid-change-type SOΣ 0..1 BackboneElement Amino Acid Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48006-1
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: Amino Acid Change Type Value Set (required)
.... component:molecular-consequence SOΣ 0..1 BackboneElement Molecular Consequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept molecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: molecular-consequence
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.
.... component:copy-number SOΣ 0..1 BackboneElement Genomic Structural Variant Copy Number
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82155-3
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣC 0..1 Quantity Actual component result
Constraints: cnt-3
.... component:variant-confidence-status OΣ 0..1 BackboneElement Variant Confidence Status
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-confidence-status
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
.... component:clinical-relevance SOΣ 1..1 BackboneElement Clinical relevance of the genomic variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: LL4034-6
....... display 1..1 string Representation defined by the system
Fixed Value: ACMG_Clinical significance of genetic variation
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 CodeableConcept Actual component result
Binding: Clinical Relevance Value Set (required)
.... component:nucleotides-count SOΣ 1..1 BackboneElement Length of of the variant in nNucleotides
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 integer Actual component result
.... component:gene-region SOΣ 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result
.... component:gene-panel-sequencing SOΣ 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C165600
....... display 1..1 string Representation defined by the system
Fixed Value: Tumor Panel Sequencing
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Sequencing Gene Panel
.... component:hgvs-version SOΣ 1..1 BackboneElement HGVS Version
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81303-0
....... display 1..1 string Representation defined by the system
Fixed Value: HGVS version [ID]
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result
.... component:rna-hgvs SOΣ 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: rna-hgvs
....... display 1..1 string Representation defined by the system
Fixed Value: Transcript RNA change (rHGVS)
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📦4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📦4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📦4.0.1 FHIR Std.
Observation.method Base extensible LOINC Answer Codes for LL4048-6 unknown?
Observation.component.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 unknown?
Observation.component:coding-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:exact-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 unknown?
Observation.component:ref-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base required Coding DNA Change Types Value Set 📦0.2.0 This IG
Observation.component:genomic-source-class.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 unknown?
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 unknown?
Observation.component:variant-inheritance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible Variant Inheritances 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variation-code.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 unknown?
Observation.component:protein-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:amino-acid-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​value[x] Base required Amino Acid Change Type Value Set 📦0.2.0 This IG
Observation.component:molecular-consequence.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:molecular-consequence.​value[x] Base extensible Molecular Consequence 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:copy-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:clinical-relevance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:clinical-relevance.​value[x] Base required Clinical Relevance Value Set 📦0.2.0 This IG
Observation.component:nucleotides-count.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-region.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-panel-sequencing.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:hgvs-version.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:rna-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
cnt-3 error Observation.component:copy-number.value[x] There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

Differential View

This structure is derived from GenomicVariant

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicVariant Variant
Constraints: o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
... Slices for extension Content/Rules for all slices
.... extension:genomic-variant-assessment-date SO 0..1 dateTime Genomic Variant Assessment Date
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... status 1..1 code Not used in this profile
... subject O 1..1 Reference(Cancer Patient Profile) Who and/or what the observation is about
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... encounter 0..1 Reference(Encounter) Not used in this profile
... effective[x] 1..1 dateTime Clinically-relevant date of the genomic variant (e.g. the specimen collection date)
... Slices for effective[x] Content/Rules for all slices
.... effective[x]:effectiveDateTime O 0..1 dateTime Clinically relevant time/time-period for observation
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... issued 0..1 instant Not used in this profile
... performer 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Not used in this profile
... interpretation 0..* CodeableConcept Not used in this profile
... bodySite 0..1 CodeableConcept Not used in this profile
... specimen 0..1 Reference(Human Specimen Profile) Not used in this profile
... device 0..1 Reference(Device | DeviceMetric) Not used in this profile
... component 4..* BackboneElement Component results
... Slices for component Content/Rules for all slices
.... component:conclusion-string 0..1 BackboneElement Not used in this profile
.... component:cytogenetic-location O 0..* BackboneElement Cytogenetic (Chromosome) Location
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:reference-sequence-assembly O 0..* BackboneElement Human Reference Sequence Assembly
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:coding-hgvs O 0..1 BackboneElement Coding (cDNA) Change - cHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T
.... component:genomic-hgvs O 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
.... component:genomic-ref-seq O 0..1 BackboneElement Genomic Reference Sequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:transcript-ref-seq O 0..1 BackboneElement Reference Transcript
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:exact-start-end O 0..1 BackboneElement Exact Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:inner-start-end O 0..1 BackboneElement Inner Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:outer-start-end O 0..1 BackboneElement Outer Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:coordinate-system O 0..1 BackboneElement Coordinate System
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:ref-allele 0..1 BackboneElement Not used in this profile
.... component:alt-allele 0..1 BackboneElement Not used in this profile
.... component:coding-change-type O 0..1 BackboneElement Coding DNA Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... value[x] 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: Coding DNA Change Types Value Set (required)
.... component:genomic-source-class O 0..1 BackboneElement Genomic Source Class
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:sample-allelic-frequency O 0..1 BackboneElement Sample Allelic Frequency
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:allelic-read-depth O 0..1 BackboneElement Allelic Read Depth
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:allelic-state O 0..1 BackboneElement Allelic State
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:variant-inheritance O 0..1 BackboneElement Variant Inheritance
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:variation-code O 0..* BackboneElement Variation Code
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:chromosome-identifier O 0..* BackboneElement Chromosome Identifier
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:protein-hgvs O 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
.... component:amino-acid-change-type O 0..1 BackboneElement Amino Acid Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... value[x] 1..1 CodeableConcept Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: Amino Acid Change Type Value Set (required)
.... component:molecular-consequence O 0..1 BackboneElement Molecular Consequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:copy-number O 0..1 BackboneElement Genomic Structural Variant Copy Number
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:variant-confidence-status O 0..1 BackboneElement Variant Confidence Status
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
.... component:clinical-relevance SO 1..1 BackboneElement Clinical relevance of the genomic variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: LL4034-6
....... display 1..1 string Representation defined by the system
Fixed Value: ACMG_Clinical significance of genetic variation
..... value[x] S 0..1 CodeableConcept Actual component result
Binding: Clinical Relevance Value Set (required)
.... component:nucleotides-count SO 1..1 BackboneElement Length of of the variant in nNucleotides
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
..... value[x] S 0..1 integer Actual component result
.... component:gene-region SO 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
..... value[x] S 0..1 string Actual component result
.... component:gene-panel-sequencing SO 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C165600
....... display 1..1 string Representation defined by the system
Fixed Value: Tumor Panel Sequencing
..... value[x] S 0..1 string Sequencing Gene Panel
.... component:hgvs-version SO 1..1 BackboneElement HGVS Version
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81303-0
....... display 1..1 string Representation defined by the system
Fixed Value: HGVS version [ID]
..... value[x] S 0..1 string Actual component result
.... component:rna-hgvs SO 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... code S 1..1 CodeableConcept Type of component observation (code / type)
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: rna-hgvs
....... display 1..1 string Representation defined by the system
Fixed Value: Transcript RNA change (rHGVS)
..... value[x] S 0..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.component:coding-change-type.​value[x] Base required Coding DNA Change Types Value Set 📦0.2.0 This IG
Observation.component:amino-acid-change-type.​value[x] Base required Amino Acid Change Type Value Set 📦0.2.0 This IG
Observation.component:clinical-relevance.​value[x] Base required Clinical Relevance Value Set 📦0.2.0 This IG

Constraints

Id Grade Path(s) Description Expression
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicVariant Variant
Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.
Additional BindingsPurpose
AllLanguages Max Binding
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
.... extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
.... extension:genomic-variant-assessment-date SO 0..1 dateTime Genomic Variant Assessment Date
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business Identifier for observation
... basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) Part of referenced event
... status ?!SΣ 1..1 code Not used in this profile
Binding: ObservationStatus (required): Codes providing the status of an observation.
... Slices for category S 1..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text 0..1 string Plain text representation of the concept
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text Σ 0..1 string Plain text representation of the concept
... code SΣ 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69548-6
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... subject SOΣ 1..1 Reference(Cancer Patient Profile) Who and/or what the observation is about
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... focus Σ 0..* Reference(Resource) Not used in this profile
... encounter Σ 0..1 Reference(Encounter) Not used in this profile
... Slices for effective[x] SΣ 1..1 dateTime Clinically-relevant date of the genomic variant (e.g. the specimen collection date)
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime SOΣ 0..1 dateTime Clinically relevant time/time-period for observation
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
... issued Σ 0..1 instant Not used in this profile
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Not used in this profile
... Slices for value[x] SΣC 0..1 CodeableConcept Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... interpretation 0..* CodeableConcept Not used in this profile
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
... note 0..* CodedAnnotation Comments about the Observation that also contain a coded type
... bodySite 0..1 CodeableConcept Not used in this profile
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
... method S 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S 0..1 Reference(Human Specimen Profile) Not used in this profile
... device 0..1 Reference(Device | DeviceMetric) Not used in this profile
... referenceRange C 0..* BackboneElement Not used in this profile
Constraints: obs-3
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... low C 0..1 SimpleQuantity Low Range, if relevant
.... high C 0..1 SimpleQuantity High Range, if relevant
.... type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
.... appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
.... age 0..1 Range Applicable age range, if relevant
.... text 0..1 string Text based reference range in an observation
... hasMember Σ 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Not used in this profile
... derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
... Slices for component SΣ 4..* BackboneElement Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
..... value[x] Σ 0..1 Actual component result
...... valueQuantity Quantity
...... valueCodeableConcept CodeableConcept
...... valueString string
...... valueBoolean boolean
...... valueInteger integer
...... valueRange Range
...... valueRatio Ratio
...... valueSampledData SampledData
...... valueTime time
...... valueDateTime dateTime
...... valuePeriod Period
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:conclusion-string Σ 0..1 BackboneElement Not used in this profile
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: conclusion-string
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Summary conclusion (interpretation/impression)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:gene-studied SΣ 0..* BackboneElement Gene Studied
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48018-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:cytogenetic-location SOΣ 0..* BackboneElement Cytogenetic (Chromosome) Location
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48001-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Example: 1q21.1
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:reference-sequence-assembly OΣ 0..* BackboneElement Human Reference Sequence Assembly
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 62374-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coding-hgvs OΣ 0..1 BackboneElement Coding (cDNA) Change - cHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-hgvs SOΣ 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81290-9
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:cytogenomic-nomenclature SΣ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81291-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-ref-seq OΣ 0..1 BackboneElement Genomic Reference Sequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48013-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:transcript-ref-seq OΣ 0..1 BackboneElement Reference Transcript
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:exact-start-end OΣ 0..1 BackboneElement Exact Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81254-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:inner-start-end OΣ 0..1 BackboneElement Inner Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81302-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Imprecise variant inner-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:outer-start-end OΣ 0..1 BackboneElement Outer Start-End
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81301-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Imprecise variant outer-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coordinate-system OΣ 0..1 BackboneElement Coordinate System
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 92822-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:ref-allele Σ 0..1 BackboneElement Not used in this profile
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:alt-allele Σ 0..1 BackboneElement Not used in this profile
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69551-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coding-change-type SOΣ 0..1 BackboneElement Coding DNA Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48019-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: Coding DNA Change Types Value Set (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-source-class SOΣ 0..1 BackboneElement Genomic Source Class
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48002-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:sample-allelic-frequency SOΣ 0..1 BackboneElement Sample Allelic Frequency
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81258-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 Quantity Relative frequency in the sample
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
...... value Σ 0..1 decimal Numerical value (with implicit precision)
...... comparator ?!Σ 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... unit Σ 0..1 string Unit representation
...... system ΣC 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
...... code Σ 0..1 code Coded form of the unit
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:allelic-read-depth OΣ 0..1 BackboneElement Allelic Read Depth
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82121-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Quantity Unfiltered count of supporting reads
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:allelic-state SOΣ 0..1 BackboneElement Allelic State
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 53034-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variant-inheritance OΣ 0..1 BackboneElement Variant Inheritance
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept variant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-inheritance
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: Variant Inheritances (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variation-code SOΣ 0..* BackboneElement Variation Code
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81252-9
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:chromosome-identifier OΣ 0..* BackboneElement Chromosome Identifier
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48000-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:protein-hgvs SOΣ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48005-3
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:amino-acid-change-type SOΣ 0..1 BackboneElement Amino Acid Change Type
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48006-1
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: Amino Acid Change Type Value Set (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:molecular-consequence SOΣ 0..1 BackboneElement Molecular Consequence
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept molecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: molecular-consequence
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:copy-number SOΣ 0..1 BackboneElement Genomic Structural Variant Copy Number
ObligationsActor
SHALL:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82155-3
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣC 0..1 Quantity Actual component result
Constraints: cnt-3
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variant-confidence-status OΣ 0..1 BackboneElement Variant Confidence Status
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-confidence-status
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:clinical-relevance SOΣ 1..1 BackboneElement Clinical relevance of the genomic variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: LL4034-6
....... display 1..1 string Representation defined by the system
Fixed Value: ACMG_Clinical significance of genetic variation
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 CodeableConcept Actual component result
Binding: Clinical Relevance Value Set (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:nucleotides-count SOΣ 1..1 BackboneElement Length of of the variant in nNucleotides
ObligationsActor
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 integer Actual component result
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:gene-region SOΣ 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
MAY:ignore Creator (Onconova)
MAY:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:gene-panel-sequencing SOΣ 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C165600
....... display 1..1 string Representation defined by the system
Fixed Value: Tumor Panel Sequencing
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Sequencing Gene Panel
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:hgvs-version SOΣ 1..1 BackboneElement HGVS Version
ObligationsActor
SHALL:populate Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81303-0
....... display 1..1 string Representation defined by the system
Fixed Value: HGVS version [ID]
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:rna-hgvs SOΣ 0..1 BackboneElement Component results
ObligationsActor
SHOULD:populate-if-known Creator (Onconova)
SHOULD:persist Consumer (Onconova)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: rna-hgvs
....... display 1..1 string Representation defined by the system
Fixed Value: Transcript RNA change (rHGVS)
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 CodeableConcept A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.language Base preferred Common Languages 📦4.0.1 FHIR Std.
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📦4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📦4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📦4.0.1 FHIR Std.
Observation.method Base extensible LOINC Answer Codes for LL4048-6 unknown?
Observation.referenceRange.​type Base preferred Observation Reference Range Meaning Codes 📦4.0.1 FHIR Std.
Observation.referenceRange.​appliesTo Base example Observation Reference Range Applies To Codes 📦4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:conclusion-string.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:gene-studied.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:gene-studied.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:coding-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:coding-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:transcript-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 unknown?
Observation.component:coordinate-system.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base required Coding DNA Change Types Value Set 📦0.2.0 This IG
Observation.component:coding-change-type.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 unknown?
Observation.component:genomic-source-class.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 unknown?
Observation.component:allelic-state.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible Variant Inheritances 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variant-inheritance.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:variation-code.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variation-code.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 unknown?
Observation.component:chromosome-identifier.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:protein-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:protein-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​value[x] Base required Amino Acid Change Type Value Set 📦0.2.0 This IG
Observation.component:amino-acid-change-type.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:molecular-consequence.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:molecular-consequence.​value[x] Base extensible Molecular Consequence 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:molecular-consequence.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:molecular-consequence.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:copy-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:copy-number.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:copy-number.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variant-confidence-status.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:clinical-relevance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:clinical-relevance.​value[x] Base required Clinical Relevance Value Set 📦0.2.0 This IG
Observation.component:clinical-relevance.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:clinical-relevance.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:nucleotides-count.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:nucleotides-count.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:nucleotides-count.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:gene-region.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-region.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:gene-region.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:gene-panel-sequencing.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:gene-panel-sequencing.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:gene-panel-sequencing.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:hgvs-version.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:hgvs-version.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:hgvs-version.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:rna-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:rna-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:rna-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
cnt-3 error Observation.component:copy-number.value[x] There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-3 error Observation.referenceRange Must have at least a low or a high or text low.exists() or high.exists() or text.exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from GenomicVariant

Summary

Mandatory: 6 elements
Must-Support: 19 elements

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

 

Other representations of profile: CSV, Excel, Schematron